Marcus Hanwell and Kyle Lutz will present two talks in the Skolnik Symposium: Molecular Science and the Semantic Web, and there will be a group poster highlighting the Open Chemistry work.
Avogadro, Open Chemistry and Chemical Semantics
Marcus D. Hanwell and Kyle Lutz
Avogadro is being rewritten and architected to put semantic chemical meaning at the center of its internal data structures in order to fully support data-centric workflows. Computational and experimental chemistry both suffer when semantic meaning is lost; through the use of expressive formats such as CML, along with lightweight data-exchange formats such as JSON, workflows that previously demanded manual intervention to retain semantic meaning can be used. Integration with projects like JUMBO and Open Babel when conversion is required, coupled with codes such as NWChem where direct support for CML is being added, allow for much richer storage, analysis, and indexing of data. As web-based data sources add more semantic structure to their data, Avogadro will take advantage of those resources.
Exploring Large Chemical Data Sets: Interactive Analysis and Visualization
Kyle Lutz and Marcus D. Hanwell
A new open-source application, ChemData, has been developed to facilitate the exploration and analysis of large chemical data sets. The program features include a variety of 2D plotting techniques, such as traditional scatter plots, parallel coordinates charts, and scatter plot matrices. Similarity relations between molecules can be explored using a range of graph-based visualization methods. Multiple querying and filtering functions allow users to locate molecular data relevant to their work. The application uses MongoDB as a semantic data store, focusing on cheminformatics and assessment of chemical properties such as QSAR data. Computational chemistry data is stored directly in the file store, and semantic data is extracted to facilitate search and analysis. Initial work is also in progress for using web-based visualization and analysis tools to interact with the data.
Open Chemistry: Realizing Open Data, Open Standards and Open Source (group poster session)
Kyle Lutz, Marcus D. Hanwell, Chris Harris and David Lonie
The Blue Obelisk has brought together the computational chemistry community and those who are passionate about Open Chemistry and realizing the promise of Open Data, Open Standards, and Open Software (ODOSOS); the three pillars the group promotes. We will present current work that has taken place over the past five years, which is inspired by these pillars, and present plans for future work.
The group is actively engaged in multiple open source projects that rely on and promote open standards and open data including: Avogadro (a powerful 3D molecular editor), OpenQube (a library for quantum mechanics), ChemData (a tool for large-scale chemical data analysis and visualization), Chemkit (a library for cheminformatics), MoleQueue (a HPC queue manager), and VTK (a library for scientific data visualization). The Open Chemistry project benefits greatly from the activities of the Blue Obelisk and makes use of several prominent open-source projects including Qt and MongoDB.